Stitch Interactive Report Run: PGDM1400_mc
Generated at 2024-09-18 23:34:29
High decoy scores
The highest scoring decoy template scores at least 50% of the actual templates in template matching. Look into the Decoy segment for more details.
Maybe the origin of this issue is one of the following:
A sample with very high background noise, in that case the result should be thoroughly checked by hand.
Incorrect segments chosen, the chosen segments should match the expected segments and species of the dataset.
Homo sapiens Heavy Chain
QVLLQQPEELVKPSQEKVSCKAPGNTLTTYDIHWVRQVPGQGLQWMGWISHEGDKKKLRKVLVERFKFTTSTPAAGLGVASTSTAYLQLSLSTSGDTAVYYCAKDLADVDVDVDALEFWGQGTAVTVSSASLRGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSTVVTVPSSSLQDKTGFCKVQLKPSNTVVEKKNEPATGTGTHTCPPCPAPELLGGPSVFLFPPKPKDTLMIPRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTLLEQGWQYNSTYRVVSVLTVLHQDWLNGKEYKGKVSNKALPAPIEKVISGLGKGQPREPQVYTLPPSRFNLVKNQVSLQDKTKGFYPSDIAVEWESNGQPENNYKTTPPVLDFDDMFFLYSKLTVDKLRWQQGNVFSCSVLHEVLHTHYTQASLSLSGPK
Depth of Coverage
Best scoring segments
Homo sapiens Light Chain
DFVLTQSPHSLSVTPGESASISCKSSHSLLHGDRSNYLAWYVQKPGRSPQLLIDLASERASGVPDRFSGSGSDKDFTLKISRVETEDVGTYYCMQGRESPWTFGQGTKVDIKRSLAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREALVNWKVDNALQSGNSQESVTEQDSKDSTYTLNSTLTLLKAYYEKHKVYACEVTHQGLSSPVTKSFGRNEC
Depth of Coverage
Best scoring segments
1288 (11.34% of all input reads) reads where matched to this segment of these 283 (21.97% of all matched reads) were matched uniquely.
592 (5.21% of all input reads) reads where matched to this segment of these 42 (7.09% of all matched reads) were matched uniquely.
| Identifier | Length | Score | Matches | Unique Score | Unique Matches |
|---|---|---|---|---|---|
| IGHG3 | 377 | 4.203E+04 | 467 | 0 | 0 |
| IGHG2 | 326 | 3.432E+04 | 381 | 64 | 1 |
| IGHG4 | 327 | 3.351E+04 | 378 | 50 | 1 |
| IGHV1-58 | 118 | 1223 | 14 | 438 | 6 |
| IGHV1-69 | 118 | 892 | 10 | 65 | 1 |
| IGHV1-69-2 | 118 | 840 | 9 | 58 | 1 |
| IGHV3-23 | 118 | 805 | 10 | 0 | 0 |
| IGHV1-8 | 118 | 769 | 8 | 45 | 1 |
| IGHV1-46 | 118 | 751 | 8 | 0 | 0 |
| IGHV1-3 | 118 | 726 | 7 | 0 | 0 |
| IGHV1-24 | 118 | 724 | 7 | 0 | 0 |
| IGHV3-NL1 | 118 | 682 | 8 | 0 | 0 |
| IGHV3-30-5 | 118 | 617 | 7 | 0 | 0 |
| IGHV3-73 | 120 | 550 | 11 | 460 | 9 |
| IGHV7-4-1 | 118 | 531 | 6 | 0 | 0 |
| IGHV2-70 | 120 | 435 | 7 | 0 | 0 |
| IGHV6-1 | 121 | 419 | 6 | 105 | 2 |
| IGHV3-48 | 118 | 366 | 6 | 0 | 0 |
| IGHV4-30-2 | 119 | 359 | 6 | 183 | 3 |
| IGHA1 | 323 | 350 | 5 | 164 | 3 |
| IGHV3-21 | 118 | 350 | 6 | 0 | 0 |
| IGHV1-45 | 118 | 339 | 5 | 0 | 0 |
| IGHV3-7 | 118 | 321 | 5 | 0 | 0 |
| IGHV3-72 | 120 | 321 | 5 | 0 | 0 |
| IGHV3-66 | 117 | 312 | 5 | 0 | 0 |
| IGHV3-53 | 117 | 312 | 5 | 0 | 0 |
| IGHV3-74 | 118 | 312 | 5 | 0 | 0 |
| IGHV3-13 | 117 | 312 | 5 | 0 | 0 |
| IGHM | 453 | 307 | 6 | 145 | 3 |
| IGHV1-2 | 118 | 300 | 6 | 152 | 3 |
| IGHV3-11 | 118 | 291 | 5 | 0 | 0 |
| IGHV3-64 | 118 | 288 | 5 | 61 | 1 |
| IGHA2 | 310 | 286 | 4 | 100 | 2 |
| IGHV4-61 | 119 | 272 | 4 | 58 | 1 |
| IGHV3-9 | 119 | 256 | 4 | 0 | 0 |
| IGHE | 428 | 235 | 5 | 45 | 1 |
| IGHD | 385 | 233 | 5 | 136 | 3 |
| IGHV4-31 | 119 | 217 | 3 | 0 | 0 |
| IGHV4-59 | 117 | 214 | 3 | 0 | 0 |
| IGHV4-28 | 118 | 199 | 3 | 0 | 0 |
| IGHV3-43 | 119 | 185 | 3 | 0 | 0 |
| IGHV3-33 | 118 | 176 | 3 | 0 | 0 |
| IGHV3-30 | 118 | 176 | 3 | 0 | 0 |
| IGHV4-4 | 118 | 163 | 3 | 0 | 0 |
| IGHV4-39 | 119 | 156 | 2 | 0 | 0 |
| IGHV4-38-2 | 118 | 156 | 2 | 0 | 0 |
| IGHV3-20 | 118 | 152 | 3 | 0 | 0 |
| IGHV3-15 | 120 | 152 | 3 | 0 | 0 |
| IGHV4-30-4 | 119 | 151 | 2 | 0 | 0 |
| IGHV2-26 | 120 | 127 | 2 | 0 | 0 |
| IGHV3-49 | 120 | 116 | 2 | 0 | 0 |
| IGHV4-34 | 117 | 115 | 2 | 0 | 0 |
| IGHV5-10-1 | 118 | 70 | 1 | 0 | 0 |
| IGHV2-5 | 120 | 56 | 1 | 0 | 0 |
| IGHJ6 | 40 | 0 | 0 | 0 | 0 |
| IGHJ2 | 37 | 0 | 0 | 0 | 0 |
| IGHJ4 | 35 | 0 | 0 | 0 | 0 |
| IGHV5-51 | 118 | 0 | 0 | 0 | 0 |
| IGHJ3 | 36 | 0 | 0 | 0 | 0 |
| IGHJ1 | 37 | 0 | 0 | 0 | 0 |
IGHV * IGHJ
...SKD--D
LADVDV...Best overlap (1, 3) with score 6 which results in the following sequence:
...SKDLADVDV...
130 (1.14% of all input reads) reads where matched to this segment of these 38 (29.23% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
| Identifier | Length | Score | Matches | Unique Score | Unique Matches |
|---|---|---|---|---|---|
| IGHV1-18 | 118 | 3223 | 44 | 548 | 7 |
| IGHV1-46 | 118 | 2927 | 38 | 0 | 0 |
| IGHV1-8 | 118 | 2613 | 34 | 119 | 2 |
| IGHV7-4-1 | 118 | 2132 | 29 | 0 | 0 |
| IGHV1-3 | 118 | 2078 | 24 | 0 | 0 |
| IGHV1-69 | 118 | 1903 | 25 | 65 | 1 |
| IGHV1-58 | 118 | 1694 | 20 | 438 | 6 |
| IGHV1-24 | 118 | 1366 | 15 | 0 | 0 |
| IGHV1-69-2 | 118 | 1261 | 14 | 58 | 1 |
| IGHV1-2 | 118 | 1142 | 19 | 152 | 3 |
| IGHV3-13 | 117 | 1086 | 18 | 0 | 0 |
| IGHV3-73 | 120 | 826 | 14 | 460 | 9 |
| IGHV3-23 | 118 | 805 | 10 | 0 | 0 |
| IGHV6-1 | 121 | 714 | 10 | 178 | 3 |
| IGHV1-45 | 118 | 695 | 11 | 45 | 1 |
| IGHV3-NL1 | 118 | 682 | 8 | 0 | 0 |
| IGHV3-30-5 | 118 | 617 | 7 | 0 | 0 |
| IGHV4-30-2 | 119 | 506 | 8 | 183 | 3 |
| IGHV2-70 | 120 | 435 | 7 | 0 | 0 |
| IGHV4-61 | 119 | 419 | 6 | 58 | 1 |
| IGHV3-48 | 118 | 366 | 6 | 0 | 0 |
| IGHV4-31 | 119 | 364 | 5 | 0 | 0 |
| IGHV4-59 | 117 | 361 | 5 | 0 | 0 |
| IGHV3-21 | 118 | 350 | 6 | 0 | 0 |
| IGHV4-28 | 118 | 346 | 5 | 0 | 0 |
| IGHV4-34 | 117 | 342 | 5 | 0 | 0 |
| IGHV3-72 | 120 | 321 | 5 | 0 | 0 |
| IGHV3-7 | 118 | 321 | 5 | 0 | 0 |
| IGHV3-53 | 117 | 312 | 5 | 0 | 0 |
| IGHV3-66 | 117 | 312 | 5 | 0 | 0 |
| IGHV3-74 | 118 | 312 | 5 | 0 | 0 |
| IGHV4-39 | 119 | 303 | 4 | 0 | 0 |
| IGHV4-38-2 | 118 | 303 | 4 | 0 | 0 |
| IGHV4-30-4 | 119 | 298 | 4 | 0 | 0 |
| IGHV3-11 | 118 | 291 | 5 | 0 | 0 |
| IGHV3-64 | 118 | 288 | 5 | 61 | 1 |
| IGHV3-9 | 119 | 256 | 4 | 0 | 0 |
| IGHV4-4 | 118 | 230 | 4 | 0 | 0 |
| IGHV3-43 | 119 | 185 | 3 | 0 | 0 |
| IGHV3-33 | 118 | 176 | 3 | 0 | 0 |
| IGHV3-30 | 118 | 176 | 3 | 0 | 0 |
| IGHV3-20 | 118 | 152 | 3 | 0 | 0 |
| IGHV3-15 | 120 | 152 | 3 | 0 | 0 |
| IGHV5-10-1 | 118 | 142 | 2 | 0 | 0 |
| IGHV2-26 | 120 | 127 | 2 | 0 | 0 |
| IGHV3-49 | 120 | 116 | 2 | 0 | 0 |
| IGHV5-51 | 118 | 72 | 1 | 0 | 0 |
| IGHV2-5 | 120 | 56 | 1 | 0 | 0 |
Scores per group
Max ScoreAverage Score
Matches per group
Matches
5 (0.04% of all input reads) reads where matched to this segment of these 0 (0.00% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
Scores per group
Max ScoreAverage ScoreUnique Max ScoreUnique Average Score
Matches per group
MatchesUnique Matches
577 (5.08% of all input reads) reads where matched to this segment of these 48 (8.32% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
All reads matching any Template within the CDR regions are listed here. These all stem from the alignments made in the TemplateMatching step.
CDR1
39 (0.34% of all input reads) distinct reads were matched on 39 (25.83% of all templates with CDRs) distinct templates, of these 14 (35.90% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
TN
LT
KL
T
.
.
T
Y
LD
KL
CDR2
36 (0.32% of all input reads) distinct reads were matched on 17 (11.26% of all templates with CDRs) distinct templates, of these 9 (25.00% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
NGS
GSH
GSDHE
EG
.
G
NEKGD
DTK
VYNK
CDR3
13 (0.11% of all input reads) distinct reads were matched on 43 (28.48% of all templates with CDRs) distinct templates, of these 0 (0.00% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
DEGK
SFD
.
.
.
.
.
.
.
.
.
.
WD
V
666 (5.86% of all input reads) reads where matched to this segment of these 329 (49.40% of all matched reads) were matched uniquely.
| Identifier | Length | Order | Score | Matches | Unique Score | Unique Matches |
|---|---|---|---|---|---|---|
| REC-0-1_002 | 219 | IGKV2-28 → IGKJ1 → IGKC | 4.527E+04 | 666 | 2.866E+04 | 329 |
191 (1.68% of all input reads) reads where matched to this segment of these 41 (21.47% of all matched reads) were matched uniquely.
| Identifier | Length | Score | Matches | Unique Score | Unique Matches |
|---|---|---|---|---|---|
| IGKV2D-29 | 100 | 2495 | 29 | 0 | 0 |
| IGKV2-40 | 101 | 1891 | 28 | 197 | 3 |
| IGKV4-1 | 101 | 1868 | 29 | 52 | 1 |
| IGKV1-27 | 95 | 1533 | 24 | 0 | 0 |
| IGKV3D-20 | 96 | 1447 | 27 | 57 | 1 |
| IGKV2D-26 | 100 | 1401 | 22 | 333 | 5 |
| IGKV2-30 | 100 | 1193 | 18 | 0 | 0 |
| IGKV2D-30 | 100 | 1141 | 17 | 0 | 0 |
| IGKV3-20 | 96 | 1128 | 21 | 0 | 0 |
| IGKV2-24 | 100 | 798 | 13 | 54 | 1 |
| IGKV3-11 | 95 | 758 | 14 | 0 | 0 |
| IGKV1D-8 | 95 | 677 | 12 | 45 | 1 |
| IGKV3D-11 | 95 | 674 | 13 | 0 | 0 |
| IGLV1-47 | 98 | 671 | 11 | 46 | 1 |
| IGLV1-44 | 98 | 671 | 11 | 0 | 0 |
| IGLC7 | 106 | 642 | 13 | 239 | 5 |
| IGLV8-61 | 98 | 590 | 11 | 262 | 5 |
| IGKV1-8 | 95 | 530 | 10 | 0 | 0 |
| IGLV4-60 | 99 | 487 | 9 | 227 | 4 |
| IGLV1-36 | 98 | 453 | 7 | 0 | 0 |
| IGLV6-57 | 98 | 423 | 8 | 217 | 4 |
| IGKV1-9 | 95 | 369 | 7 | 0 | 0 |
| IGKV3D-7 | 96 | 339 | 7 | 0 | 0 |
| IGKV1-16 | 95 | 338 | 6 | 0 | 0 |
| IGKV1-12 | 95 | 322 | 6 | 0 | 0 |
| IGKJ3 | 12 | 307 | 5 | 0 | 0 |
| IGKV1-33 | 95 | 292 | 5 | 66 | 1 |
| IGLV2-23 | 99 | 291 | 5 | 73 | 1 |
| IGKJ2 | 12 | 284 | 5 | 0 | 0 |
| IGKV1D-16 | 95 | 275 | 5 | 0 | 0 |
| IGKV1-NL1 | 95 | 267 | 5 | 0 | 0 |
| IGKV1-6 | 95 | 260 | 5 | 0 | 0 |
| IGKV1-39 | 95 | 260 | 5 | 0 | 0 |
| IGLV2-18 | 99 | 254 | 5 | 0 | 0 |
| IGLV2-11 | 99 | 254 | 5 | 0 | 0 |
| IGKV1D-43 | 95 | 254 | 5 | 0 | 0 |
| IGKV3-15 | 95 | 253 | 5 | 0 | 0 |
| IGKV1D-13 | 95 | 222 | 4 | 0 | 0 |
| IGLV2-14 | 99 | 218 | 4 | 0 | 0 |
| IGLV3-10 | 96 | 184 | 3 | 0 | 0 |
| IGLV3-27 | 94 | 182 | 3 | 0 | 0 |
| IGLC2 | 106 | 177 | 3 | 0 | 0 |
| IGLC6 | 106 | 177 | 3 | 0 | 0 |
| IGLC3 | 104 | 177 | 3 | 0 | 0 |
| IGLV10-54 | 98 | 166 | 3 | 118 | 2 |
| IGLV1-51 | 98 | 163 | 3 | 45 | 1 |
| IGLV4-69 | 99 | 161 | 3 | 61 | 1 |
| IGKV5-2 | 95 | 154 | 3 | 109 | 2 |
| IGLV2-8 | 99 | 152 | 3 | 0 | 0 |
| IGLV1-40 | 99 | 142 | 3 | 0 | 0 |
| IGLV5-45 | 104 | 121 | 2 | 45 | 1 |
| IGKV1D-17 | 95 | 118 | 2 | 0 | 0 |
| IGLV3-19 | 96 | 116 | 2 | 0 | 0 |
| IGLV3-16 | 96 | 111 | 2 | 0 | 0 |
| IGLV5-52 | 105 | 89 | 2 | 37 | 1 |
| IGLV5-39 | 104 | 84 | 1 | 0 | 0 |
| IGLV3-25 | 96 | 66 | 1 | 0 | 0 |
| IGKV1-5 | 95 | 62 | 1 | 0 | 0 |
| IGKJ5 | 12 | 61 | 1 | 0 | 0 |
| IGLV3-21 | 96 | 60 | 1 | 0 | 0 |
| IGLJ7 | 12 | 55 | 1 | 0 | 0 |
| IGKV1-17 | 95 | 55 | 1 | 0 | 0 |
| IGKV6-21 | 95 | 54 | 1 | 0 | 0 |
| IGLV7-46 | 98 | 52 | 1 | 0 | 0 |
| IGLV5-37 | 104 | 52 | 1 | 0 | 0 |
| IGLV3-22 | 94 | 0 | 0 | 0 | 0 |
| IGLV7-43 | 98 | 0 | 0 | 0 | 0 |
| IGLV3-9 | 95 | 0 | 0 | 0 | 0 |
| IGLJ6 | 12 | 0 | 0 | 0 | 0 |
| IGKJ4 | 12 | 0 | 0 | 0 | 0 |
| IGLJ2 | 12 | 0 | 0 | 0 | 0 |
| IGLV3-1 | 95 | 0 | 0 | 0 | 0 |
| IGLJ1 | 12 | 0 | 0 | 0 | 0 |
265 (2.33% of all input reads) reads where matched to this segment of these 74 (27.92% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
| Identifier | Length | Score | Matches | Unique Score | Unique Matches |
|---|---|---|---|---|---|
| IGKV2-28 | 100 | 7694 | 99 | 1466 | 21 |
| IGKV2D-29 | 100 | 6925 | 78 | 1052 | 11 |
| IGKV2-40 | 101 | 4760 | 59 | 208 | 3 |
| IGKV2D-26 | 100 | 3186 | 46 | 333 | 5 |
| IGKV2-30 | 100 | 2823 | 40 | 0 | 0 |
| IGKV2D-30 | 100 | 2771 | 39 | 0 | 0 |
| IGKV4-1 | 101 | 2663 | 43 | 52 | 1 |
| IGKV3D-20 | 96 | 2480 | 43 | 57 | 1 |
| IGKV3-20 | 96 | 2053 | 37 | 167 | 3 |
| IGKV1-27 | 95 | 1885 | 30 | 0 | 0 |
| IGKV2-24 | 100 | 1161 | 18 | 54 | 1 |
| IGKV3-11 | 95 | 1135 | 20 | 0 | 0 |
| IGKV3D-11 | 95 | 932 | 17 | 0 | 0 |
| IGLV1-44 | 98 | 881 | 14 | 0 | 0 |
| IGLV1-47 | 98 | 881 | 14 | 46 | 1 |
| IGKV1D-8 | 95 | 848 | 15 | 45 | 1 |
| IGKV3-15 | 95 | 834 | 13 | 0 | 0 |
| IGKV1-8 | 95 | 701 | 13 | 0 | 0 |
| IGLV6-57 | 98 | 693 | 11 | 217 | 4 |
| IGKV3D-7 | 96 | 681 | 13 | 0 | 0 |
| IGLV1-36 | 98 | 663 | 10 | 0 | 0 |
| IGKV1-33 | 95 | 651 | 11 | 187 | 3 |
| IGLV8-61 | 98 | 590 | 11 | 262 | 5 |
| IGKV1-12 | 95 | 493 | 9 | 0 | 0 |
| IGLV4-60 | 99 | 487 | 9 | 227 | 4 |
| IGKV1-16 | 95 | 457 | 8 | 0 | 0 |
| IGKV1-9 | 95 | 457 | 9 | 0 | 0 |
| IGKV1-6 | 95 | 431 | 8 | 0 | 0 |
| IGKV1-39 | 95 | 431 | 8 | 0 | 0 |
| IGLV5-45 | 104 | 409 | 6 | 45 | 1 |
| IGKV1D-16 | 95 | 394 | 7 | 0 | 0 |
| IGKV1D-13 | 95 | 393 | 7 | 0 | 0 |
| IGLV2-18 | 99 | 353 | 6 | 0 | 0 |
| IGKV1-NL1 | 95 | 319 | 6 | 0 | 0 |
| IGLV2-14 | 99 | 317 | 5 | 0 | 0 |
| IGLV3-1 | 95 | 305 | 4 | 0 | 0 |
| IGLV3-27 | 94 | 303 | 5 | 0 | 0 |
| IGLV5-39 | 104 | 294 | 4 | 0 | 0 |
| IGLV2-23 | 99 | 291 | 5 | 73 | 1 |
| IGLV1-51 | 98 | 285 | 5 | 45 | 1 |
| IGLV5-37 | 104 | 262 | 4 | 0 | 0 |
| IGLV10-54 | 98 | 261 | 4 | 118 | 2 |
| IGKV1D-43 | 95 | 254 | 5 | 0 | 0 |
| IGLV2-11 | 99 | 254 | 5 | 0 | 0 |
| IGLV3-16 | 96 | 232 | 4 | 0 | 0 |
| IGKV6-21 | 95 | 209 | 4 | 0 | 0 |
| IGLV4-69 | 99 | 197 | 4 | 61 | 1 |
| IGLV3-25 | 96 | 187 | 3 | 0 | 0 |
| IGLV3-10 | 96 | 184 | 3 | 0 | 0 |
| IGKV5-2 | 95 | 154 | 3 | 154 | 3 |
| IGLV2-8 | 99 | 152 | 3 | 0 | 0 |
| IGLV1-40 | 99 | 142 | 3 | 0 | 0 |
| IGKV1D-17 | 95 | 118 | 2 | 0 | 0 |
| IGLV3-19 | 96 | 116 | 2 | 0 | 0 |
| IGKV1-5 | 95 | 114 | 2 | 0 | 0 |
| IGLV5-52 | 105 | 89 | 2 | 37 | 1 |
| IGLV3-9 | 95 | 74 | 1 | 0 | 0 |
| IGLV3-21 | 96 | 60 | 1 | 0 | 0 |
| IGKV1-17 | 95 | 55 | 1 | 0 | 0 |
| IGLV7-46 | 98 | 52 | 1 | 0 | 0 |
| IGLV7-43 | 98 | 0 | 0 | 0 | 0 |
| IGLV3-22 | 94 | 0 | 0 | 0 | 0 |
Scores per group
Max ScoreAverage ScoreUnique Max ScoreUnique Average Score
Matches per group
MatchesUnique Matches
45 (0.40% of all input reads) reads where matched to this segment of these 13 (28.89% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
149 (1.31% of all input reads) reads where matched to this segment of these 133 (89.26% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
All reads matching any Template within the CDR regions are listed here. These all stem from the alignments made in the TemplateMatching step.
CDR1
55 (0.48% of all input reads) distinct reads were matched on 29 (14.80% of all templates with CDRs) distinct templates, of these 9 (16.36% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
DLSN
DYLN
L
H
G
.
D
.
N
LRY
YL
CDR2
59 (0.52% of all input reads) distinct reads were matched on 30 (15.31% of all templates with CDRs) distinct templates, of these 27 (45.76% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
DGSA
TAS
.
FTSE
CDR3
63 (0.55% of all input reads) distinct reads were matched on 20 (10.20% of all templates with CDRs) distinct templates, of these 14 (22.22% of all matched reads) were matched uniquely (on a single template). The consensus sequence is shown below.
GKQT
G
.
.
.
DRF
Scores per group
Max ScoreAverage ScoreUnique Max ScoreUnique Average Score
Matches per group
MatchesUnique Matches
2989 (26.32% of all input reads) reads where matched to this segment of these 2870 (96.02% of all matched reads) were matched uniquely.
Scores per group
Max ScoreAverage ScoreUnique Max ScoreUnique Average Score
Matches per group
MatchesUnique Matches
2989 (26.32% of all input reads) reads where matched to this segment of these 2871 (96.05% of all matched reads) were matched uniquely.
Cumulative value of all children (excluding unique)
Cumulative value for unique matches
Length distribution
/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/batchfiles/PGDM1400_mc.txt
-Run Info---------------
Version : 1.5
- Here the input can be defined, this will be used in the TemplateMatching and Recombine steps
Input ->
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3613.mztab
Name : EH3613
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3614.mztab
Name : EH3614
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3615.mztab
Name : EH3615
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3616.mztab
Name : EH3616
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3617.mztab
Name : EH3617
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3618.mztab
Name : EH3618
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3620.mztab
Name : EH3620
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3621.mztab
Name : EH3621
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3946.mztab
Name : EH3946
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3947.mztab
Name : EH3947
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3948.mztab
Name : EH3948
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3949.mztab
Name : EH3949
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3950.mztab
Name : EH3950
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3951.mztab
Name : EH3951
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3952.mztab
Name : EH3952
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3953.mztab
Name : EH3953
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3954.mztab
Name : EH3954
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3955.mztab
Name : EH3955
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3956.mztab
Name : EH3956
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH3957.mztab
Name : EH3957
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4290.mztab
Name : EH4290
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4291.mztab
Name : EH4291
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4292.mztab
Name : EH4292
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4293.mztab
Name : EH4293
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4294.mztab
Name : EH4294
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4295.mztab
Name : EH4295
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4296.mztab
Name : EH4296
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4297.mztab
Name : EH4297
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4298.mztab
Name : EH4298
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4299.mztab
Name : EH4299
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4300.mztab
Name : EH4300
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4301.mztab
Name : EH4301
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4639.mztab
Name : EH4639
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4640.mztab
Name : EH4640
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4641.mztab
Name : EH4641
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4643.mztab
Name : EH4643
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4644.mztab
Name : EH4644
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4646.mztab
Name : EH4646
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4647.mztab
Name : EH4647
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4649.mztab
Name : EH4649
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH4650.mztab
Name : EH4650
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5055.mztab
Name : EH5055
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5056.mztab
Name : EH5056
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5057.mztab
Name : EH5057
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5058.mztab
Name : EH5058
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5059.mztab
Name : EH5059
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5060.mztab
Name : EH5060
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5061.mztab
Name : EH5061
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5062.mztab
Name : EH5062
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5063.mztab
Name : EH5063
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5064.mztab
Name : EH5064
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5065.mztab
Name : EH5065
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5066.mztab
Name : EH5066
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5393.mztab
Name : EH5393
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5394.mztab
Name : EH5394
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5395.mztab
Name : EH5395
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5396.mztab
Name : EH5396
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5397.mztab
Name : EH5397
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5398.mztab
Name : EH5398
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5399.mztab
Name : EH5399
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5400.mztab
Name : EH5400
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5401.mztab
Name : EH5401
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5402.mztab
Name : EH5402
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5403.mztab
Name : EH5403
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5404.mztab
Name : EH5404
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5754.mztab
Name : EH5754
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5755.mztab
Name : EH5755
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5756.mztab
Name : EH5756
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5757.mztab
Name : EH5757
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5758.mztab
Name : EH5758
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5759.mztab
Name : EH5759
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5760.mztab
Name : EH5760
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5761.mztab
Name : EH5761
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5762.mztab
Name : EH5762
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5763.mztab
Name : EH5763
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5764.mztab
Name : EH5764
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH5765.mztab
Name : EH5765
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6112.mztab
Name : EH6112
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6113.mztab
Name : EH6113
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6114.mztab
Name : EH6114
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6115.mztab
Name : EH6115
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6116.mztab
Name : EH6116
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6117.mztab
Name : EH6117
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6118.mztab
Name : EH6118
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6119.mztab
Name : EH6119
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6120.mztab
Name : EH6120
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6121.mztab
Name : EH6121
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6122.mztab
Name : EH6122
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6123.mztab
Name : EH6123
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6643.mztab
Name : EH6643
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6644.mztab
Name : EH6644
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6645.mztab
Name : EH6645
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6646.mztab
Name : EH6646
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6647.mztab
Name : EH6647
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6648.mztab
Name : EH6648
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6649.mztab
Name : EH6649
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6650.mztab
Name : EH6650
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6651.mztab
Name : EH6651
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6652.mztab
Name : EH6652
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6653.mztab
Name : EH6653
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH6654.mztab
Name : EH6654
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8133.mztab
Name : EH8133
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8134.mztab
Name : EH8134
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8135.mztab
Name : EH8135
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8136.mztab
Name : EH8136
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8137.mztab
Name : EH8137
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8138.mztab
Name : EH8138
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8139.mztab
Name : EH8139
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8140.mztab
Name : EH8140
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8141.mztab
Name : EH8141
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8142.mztab
Name : EH8142
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8143.mztab
Name : EH8143
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8144.mztab
Name : EH8144
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7363.mztab
Name : EH7363
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7364.mztab
Name : EH7364
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7365.mztab
Name : EH7365
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7366.mztab
Name : EH7366
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7367.mztab
Name : EH7367
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7368.mztab
Name : EH7368
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7369.mztab
Name : EH7369
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7370.mztab
Name : EH7370
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7371.mztab
Name : EH7371
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7372.mztab
Name : EH7372
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7373.mztab
Name : EH7373
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7374.mztab
Name : EH7374
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7708.mztab
Name : EH7708
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7709.mztab
Name : EH7709
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7710.mztab
Name : EH7710
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7711.mztab
Name : EH7711
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7712.mztab
Name : EH7712
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7713.mztab
Name : EH7713
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7714.mztab
Name : EH7714
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7715.mztab
Name : EH7715
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7716.mztab
Name : EH7716
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7717.mztab
Name : EH7717
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7718.mztab
Name : EH7718
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH7719.mztab
Name : EH7719
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8476.mztab
Name : EH8476
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8477.mztab
Name : EH8477
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8478.mztab
Name : EH8478
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8479.mztab
Name : EH8479
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8480.mztab
Name : EH8480
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8481.mztab
Name : EH8481
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8482.mztab
Name : EH8482
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8483.mztab
Name : EH8483
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8484.mztab
Name : EH8484
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8485.mztab
Name : EH8485
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8486.mztab
Name : EH8486
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8487.mztab
Name : EH8487
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8978.mztab
Name : EH8978
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8979.mztab
Name : EH8979
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH8980.mztab
Name : EH8980
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9313.mztab
Name : EH9313
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9314.mztab
Name : EH9314
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9315.mztab
Name : EH9315
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9316.mztab
Name : EH9316
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9317.mztab
Name : EH9317
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9318.mztab
Name : EH9318
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9319.mztab
Name : EH9319
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9320.mztab
Name : EH9320
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9321.mztab
Name : EH9321
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9322.mztab
Name : EH9322
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9323.mztab
Name : EH9323
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9324.mztab
Name : EH9324
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9691.mztab
Name : EH9691
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9692.mztab
Name : EH9692
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9693.mztab
Name : EH9693
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9694.mztab
Name : EH9694
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9695.mztab
Name : EH9695
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9696.mztab
Name : EH9696
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9697.mztab
Name : EH9697
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9698.mztab
Name : EH9698
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9699.mztab
Name : EH9699
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9700.mztab
Name : EH9700
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9701.mztab
Name : EH9701
CutoffScore: 0.8
-FilterPPM : 100
<-
Casanovo ->
Path : /storage/khangl/MS_benchmarking/Casanovo_output/EH9702.mztab
Name : EH9702
CutoffScore: 0.8
-FilterPPM : 100
<-
<-
- Template matching matches the reads defined in 'Input' to the given Templates defined in the different groups in the 'Segments'
TemplateMatching ->
EnforceUnique : 0.9
CutoffScore : 15
AmbiguityThreshold : 0.9
include!(/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/alphabets/mass_alphabet.txt)
Segments->
include!(/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/Homo_sapiens_Heavy_Chain.txt)
include!(/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/Homo_sapiens_Light_Chain.txt)
include!(/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/common_contaminants.txt)
<-
<-
Recombine->
-Pick the highest scoring templates from each segment
N : 1
Decoy : True
CutoffScore : 10
-Separated by whitespace means directly attached
-Separated by * means with a gap attached
Order->
Homo sapiens Heavy Chain: IGHV * IGHJ IGHC
Homo sapiens Light Chain: IGLV IGLJ IGLC
<-
<-
Report ->
Folder: /storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/results/{datetime} {name}/
HTML ->
Path: report-monoclonal_PGDM1400.html
<-
FASTA ->
Path: report-monoclonal-tm_PGDM1400.fasta
OutputType: TemplateMatching
<-
CSV ->
Path: report-monoclonal-tm_PGDM1400.csv
OutputType: TemplateMatching
<-
FASTA ->
Path: report-monoclonal-rec_PGDM1400.fasta
OutputType: Recombine
<-
CSV ->
Path: report-monoclonal-rec_PGDM1400.csv
OutputType: Recombine
<-
<-
/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/alphabets/mass_alphabet.txt
Alphabet ->
Characters : ARNDCQEGHILKMFPSTWYVBZXJ.*
Identity : 8
Mismatch : -1
GapStart : -12
GapExtend : -1
PatchLength: 3
Swap : 2
Symmetric sets ->
Score: 8
Sets :>
I,L,J
<:
<-
Symmetric sets ->
Score: 6
Sets :>
N,GG
Q,AG
AV,GL,GI,GJ
AN,QG,AGG
LS,IS,JS,TV
AM,CV
NV,AAA,GGV
NT,QS,AGS,GGT
LN,IN,JN,QV,AGV,GGL,GGI,GGJ
DL,DI,DJ,EV
QT,AAS,AGT
AY,FS
LQ,IQ,AAV,AGL,AGI,AGJ
NQ,ANG,QGG
KN,GGK
EN,DQ,ADG,EGG
DK,AAT,GSV
MN,AAC,GGM
AS,GT
AAL,AAI,AAJ,GVV
QQ,AAN,AQG
EQ,AAD,AEG
EK,ASV,GLS,GIS,GJS,GTV
MQ,AGM,CGV
AAQ,NGV
<:
<-
Asymmetric sets ->
Score: 1
Sets :>
X->A,R,N,D,C,Q,E,G,H,I,L,J,K,M,F,P,S,T,W,Y,V,B,Z -Remove mismatch penalty on single gaps
A,R,N,D,C,Q,E,G,H,I,L,J,K,M,F,P,S,T,W,Y,V,B,Z->X -Remove mismatch penalty on single gaps
<:
<-
Asymmetric sets ->
Score: -4
Sets :>
.->A,R,N,D,C,Q,E,G,H,I,L,J,K,M,F,P,S,T,W,Y,V,B,Z -Add additional penalty on bigger gaps
A,R,N,D,C,Q,E,G,H,I,L,J,K,M,F,P,S,T,W,Y,V,B,Z->. -Add additional penalty on bigger gaps
<:
<-
Asymmetric sets ->
Score: 3
Sets :>
- Template sequence -- results -> in read sequence - Type
Q->E -Deamidation
N,GG->D -Deamidation
T->D -Methylation
S->T -Methylation
D->E -Methylation
R->AV,GL,GI,GJ -Methylation
Q->AA -Methylation
W->DS,AM,CV,TT -Oxidation
M->F -Oxidation
S->E -Acetylation
K->AV,GL,GI,GJ -Acetylation/Homoarginine
<:
<-
<-
/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/Homo_sapiens_Heavy_Chain.txt
Homo sapiens Heavy Chain->
Segment->
Path : Homo_sapiens_IGHV.fasta
Name : IGHV
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
Segment->
Path : Homo_sapiens_IGHJ.fasta
Name : IGHJ
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
Segment->
Path : Homo_sapiens_IGHC.fasta
Name : IGHC
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
<-
/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/Homo_sapiens_Light_Chain.txt
Homo sapiens Light Chain->
Segment->
Path : Homo_sapiens_IGKV,IGLV.fasta
Name : IGLV
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
Segment->
Path : Homo_sapiens_IGKJ,IGLJ.fasta
Name : IGLJ
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
Segment->
Path : Homo_sapiens_IGKC,IGLC.fasta
Name : IGLC
Identifier: ^(([a-zA-Z]+\d*)[\w-]*)
<-
<-
/storage/khangl/MS_benchmarking/stitch-v1.5.0-linux/templates/common_contaminants.txt
Decoy ->
Segment ->
Path: common_contaminants.fasta
Name: Decoy
Identifier: ^sp\|[\w]*\|([\w]+)_
<-
<-
Answers to common questions can be found here. If anything is unclear, or you miss any features please reach out to the authors, all information can be found on the repository.
If the graphs are needed in a vector graphics format the whole page can be printed to a pdf. To do this print the page to a pdf file and save the generated file. These files can be imported in most vector graphics editors. It is best to turn on the background graphics and turn off any headers, besides this setting the margins smaller and using landscape or portrait could enhance the results. See the below picture for the options. If you want to be able to edit the text as text in Adobe Illustrator we had the best results using Firefox > Print > Save as PDF.
Or click here to print
The Roepstorff, Fohlman, Johnson ion nomenclature is used. This is the common way of naming ions most people will be familiar with. But we use two special ions, w and d also called satellite ions, which are not commonly used. These form by cleavages of the side chain and are thus specially suited for the disambiguation of Leucine and Isoleucine. In the overview below the mass differences and ions formed are displayed. The d ion is formed by fragmentation of the side chain of an a ion. The w ion is formed by side chain fragmentation of a z ion. Because isoleucine and threonine are doubly substituted at the beta carbon these two amino acids form two different w/d ions. THese ions are not formed with all fragmentation techniques though, Stitch only searches for d ions in the first amino acids with CID/HCD/PQD data, and only searches for w ions in ETD/ECD/EThcD/ETciD data.
Find more information here.